Context-dependent regulation of receptor tyrosine kinases: Insights from systems biology approaches

Computational Characterization of Membrane Proteins as Anticancer Targets: Current Challenges and Opportunities

Cancer remains a leading cause of mortality worldwide and calls for novel therapeutic targets. Membrane proteins are key players in various cancer types but present unique challenges compared to soluble proteins. The advent of computational drug discovery tools offers a promising approach to address these challenges, allowing for the prioritization of "wet-lab" experiments. In this review, we explore the applications of computational approaches in membrane protein oncological characterization, particularly focusing on three prominent membrane protein families: receptor tyrosine kinases (RTKs), G protein-coupled receptors (GPCRs), and solute carrier proteins (SLCs). We chose these families due to their varying levels of understanding and research data availability, which leads to distinct challenges and opportunities for computational analysis. We discuss the utilization of multi-omics data, machine learning, and structure-based methods to investigate aberrant protein functionalities associated with cancer progression within each family. Moreover, we highlight the importance of considering the broader cellular context and, in particular, cross-talk between proteins. Despite existing challenges, computational tools hold promise in dissecting membrane protein dysregulation in cancer. With advancing computational capabilities and data resources, these tools are poised to play a pivotal role in identifying and prioritizing membrane proteins as personalized anticancer targets.

Receptor Tyrosine Kinase: Still an Interesting Target to Inhibit the Proliferation of Vascular Smooth Muscle Cells

Vascular smooth muscle cells (VSMCs) proliferation is a critical event that contributes to the pathogenesis of vascular remodeling such as hypertension, restenosis, and pulmonary hypertension. Increasing evidences have revealed that VSMCs proliferation is associated with the activation of receptor tyrosine kinases (RTKs) by their ligands, including the insulin-like growth factor receptor (IGFR), fibroblast growth factor receptor (FGFR), epidermal growth factor receptor (EGFR), vascular endothelial growth factor receptor (VEGFR), and platelet-derived growth factor receptor (PDGFR). Moreover, some receptor tyrosinase inhibitors (TKIs) have been found and can prevent VSMCs proliferation to attenuate vascular remodeling. Therefore, this review will describe recent research progress on the role of RTKs and their inhibitors in controlling VSMCs proliferation, which helps to better understand the function of VSMCs proliferation in cardiovascular events and is beneficial for the prevention and treatment of vascular disease.

Combining Multikinase Tyrosine Kinase Inhibitors Targeting the Vascular Endothelial Growth Factor and Cluster of Differentiation 47 Signaling Pathways Is Predicted to Increase the Efficacy of Antiangiogenic Combination Therapies

Angiogenesis is a critical step in tumor growth, development, and invasion. Nascent tumor cells secrete vascular endothelial growth factor (VEGF) that significantly remodels the tumor microenvironment through interaction with multiple receptors on vascular endothelial cells, including type 2 VEGF receptor (VEGFR2). The complex pathways initiated by VEGF binding to VEGFR2 lead to enhanced proliferation, survival, and motility of vascular endothelial cells and formation of a new vascular network, enabling tumor growth. Antiangiogenic therapies that inhibit VEGF signaling pathways were among the first drugs that targeted stroma rather than tumor cells. Despite improvements in progression-free survival and higher response rates relative to chemotherapy in some types of solid tumors, the impact on overall survival (OS) has been limited, with the majority of tumors eventually relapsing due to resistance or activation of alternate angiogenic pathways. Here, we developed a molecularly detailed computational model of endothelial cell signaling and angiogenesis-driven tumor growth to investigate combination therapies targeting different nodes of the endothelial VEGF/VEGFR2 signaling pathway. Simulations predicted a strong threshold-like behavior in extracellular signal-regulated kinases 1/2 (ERK1/2) activation relative to phosphorylated VEGFR2 levels, as continuous inhibition of at least 95% of receptors was necessary to abrogate phosphorylated ERK1/2 (pERK1/2). Combinations with mitogen-activated protein kinase/ERK kinase (MEK) and spingosine-1-phosphate inhibitors were found to be effective in overcoming the ERK1/2 activation threshold and abolishing activation of the pathway. Modeling results also identified a mechanism of resistance whereby tumor cells could reduce pERK1/2 sensitivity to inhibitors of VEGFR2 by upregulation of Raf, MEK, and sphingosine kinase 1 (SphK1), thus highlighting the need for deeper investigation of the dynamics of the crosstalk between VEGFR2 and SphK1 pathways. Inhibition of VEGFR2 phosphorylation was found to be more effective at blocking protein kinase B, also known as AKT, activation; however, to effectively abolish AKT activation, simulations identified Axl autophosphorylation or the Src kinase domain as potent targets. Simulations also supported activating cluster of differentiation 47 (CD47) on endothelial cells as an effective combination partner with tyrosine kinase inhibitors to inhibit angiogenesis signaling and tumor growth. Virtual patient simulations supported the effectiveness of CD47 agonism in combination with inhibitors of VEGFR2 and SphK1 pathways. Overall, the rule-based system model developed here provides new insights, generates novel hypothesis, and makes predictions regarding combinations that may enhance the OS with currently approved antiangiogenic therapies.